Egypt’s sudden military-enforced transition from the reign of former President Mohamed Morsi continued on Thursday as Adli Mansour was sworn in as interim president while the security crackdown on Morsi’s Muslim Brotherhood deepened with the arrest of most of the Brotherhood’s senior leadership.

Mansour, a 67-year-old longtime judge with a previously low public profile, was originally meant to be sworn as new head of the Supreme Constitutional Court on July 1. But that was delayed after massive nationwide anti-Morsi protests on June 30 tipped the country into political crisis, so Thursday’s ceremony was turned into a double header.

During the swearing-in, military jets flew in formation over Tahrir Square trailing colored smoke to form an airborne Egyptian flag.

In his subsequent address to the nation, Mansour—who many Egyptians had never heard speak before today—tried to paint the transition as a necessary adjustment to bring Egypt back onto the path set by the January 2011 revolution, which ousted entrenched dictator Hosni Mubarak.

Mansour said he had been given the authority and the mission, “to amend and correct the revolution of the 25th of January 2011.”

“The most glorious thing about June 30″—referring to Sunday’s massed anti-Morsi protests—”is that it brought together everyone without discrimination or division,” he said. “I offer my greetings to the revolutionary people of Egypt.” When asked if the Muslim Brotherhood would be included in whatever future coalition government is created, Mansour said, “Nobody will be excluded, and if they respond to the invitation, they will be welcomed.”

But that inclusive vision seemed increasingly unlikely on Thursday as the venerable Islamist organization vowed not to recognize or work with the new government. Thousands of Brotherhood supporters remain gathered outside the Rabaa Adaweya Mosque in the Cairo district of Nasr City, and the group announced plans for an indefinite sit-in.

Security forces surrounded the site Wednesday evening; they have made no moves to disperse the estimated 10,000 Brotherhood supporters, and appear to be allowing new people to join. At least 10 people were killed overnight Wednesday in clashes between supporters and opponents of Morsi around the country. The total death toll since the crisis began on June 30 is at least 35 — including 16 in a particularly bloody clash near Cairo University on Tuesday.

Morsi and most of his senior advisers remain detained by the military at an undisclosed location. At least a dozen senior Brotherhood officials have been arrested or detained. No formal charges have been filed. And the public rout of the Brotherhood leadership accelerated further on Thursday with the news that Supreme Guide Mohammed Badea and his deputy Kheirat Al Shater has also been arrested. Badea—the ultimate decision-maker inside the Brotherhood’s paramilitary internal structure—was reportedly arrested in the northwest corner of Egypt not far from the Libyan border. Libyan media reported that he was detained in a failed attempted to flee Egypt into Libya.

The arrest seem certain to deepen the paranoia gripping the Muslim Brotherhood—which, after decades of existence as an oppressed, clandestine movement dramatically rose to power last year. Their sudden overthrow has left them isolated and embittered. Nine cabinet ministers belonging to the Brotherhood’s Freedom and Justice Party announced their resignations Thursday in protest over what they labeled an anti-democratic military coup. The Brotherhood also called for mass demonstrations Friday in support of Morsi, but a statement on the group’s website asked its cadres, “to show restraint and commitment to peacefulness.” But there are already signs that this loss is radicalizing elements of the Morsi support base and driving some to talk openly of violence. On one of Egypt’s satellite channels last night, an unnamed man in the Morsi crowd openly told his interviewer: “I tell Al-Sissi: know that you have created a new Taliban and a new al-Qaeda in Egypt … You’ve created new mujahideen and new martyrs.”

The Brotherhood purge is already drawing negative attention in some international circles. Human Rights Watch released a detailed statement decrying, “A return to Mubarak-era practices of mass arrests and politically-motivated imprisonment of Muslim Brotherhood leaders.”

The group also noted that several Brotherhood-affiliated satellite TV stations were taken off the air immediately after Defense Minister Abdel Fatah Al-Sissi announced Morsi’s ouster Wednesday night. The Freedom and Justice Party complained on Thursday that its daily newspaper had been prevented from publishing.

Joe Stork, HRW’s deputy Middle East director, said, “One test of whether Egypt can return to a path of democratic development will rest on whether the Freedom and Justice Party can operate without political reprisals against its members.”

Other international reaction to Morsi’s removal was decidedly mixed.

U.S. President Barack Obama announced in a statement that he was “deeply concerned” by the developments and called on the Egyptian military to “move quickly and responsibly to return full authority back to a democratically elected civilian government as soon as possible through an inclusive and transparent process.” Obama also called on the military to “to avoid any arbitrary arrests of President Morsi and his supporters.”

Washington’s concerns have been duly noted (and angrily dismissed) by many of the activist forces that called for Morsi’s downfall. Opposition groups here have bristled for months over what they perceived as American support for the Morsi administration and the Brotherhood.

On Thursday, the daily newspaper Al-Tahrir took the unusual step of printing a front page headline in English that was clearly directed straight at Obama: “It’s a Revolution … Not a Coup, Mr. Obama!”

Other foreign governments were far less circumspect.

“This is a major setback for democracy in Egypt. It is urgent that Egypt return as quickly as possible to the constitutional order… there is a real danger that the democratic transition in Egypt will be seriously damaged,” said German Foreign Minister Guido Westerwelle.

Turkish Deputy Prime Minister Bekir Bozdag said, “The power change in Egypt was not a result of the will of the people. The change was not in compliance with democracy and law.”

And no less an international relations authority than Syrian President Bashar Assad also weighed in on the abrupt downfall of the man who recently severed relations and repeatedly called for Assad’s own removal.

“What is happening in Egypt is the fall of what is known as political Islam,” Assad said in an interview with Syrian state newspaper Al-Thawra. “After a whole year, reality has become clear to the Egyptian people. The Muslim Brotherhood’s performance has helped them see the lies the [movement] used at the start of the popular revolution in Egypt.”